The Department of Conservation said they were alerted last night about a mass stranding of whales at Hanson Bay, near the township of Owenga in the Chatham Islands.

Staff were unable to assess the situation in the dark and returned this morning to find 30-40 pilot whales had re-floated themselves and returned to the sea but 50 out of the 51 whales that remained on the shore had died.

That one whale has since been put down.

"There was no likelihood of being able to successfully save the remaining whale. Sadly, the decision was made to euthanise. It was the most humane thing to do," DOC Chatham Islands Operations Manager Dave Carlton said.

"This is always an awful decision to have to make."

Local Moriori imi and Ngāti Mutunga iwi have been notified and locals will help to bury them at the site.